On Fri, Oct 29, 2010 at 12:14 PM, Sunny Srivastava <research.baba@gmail.com>wrote: > Hello Thomas, > I am sure senior members of the list will have more to say, here is my > $0.02. > > logFC is the coefficient of the treatment in your model. Assuming that you > have a model with only one treatment > > log Int_g = b0 + b1 * trt > > b1 = logFC > > The CI of logFC can be found in the same manner as you would do in normal > linear regression, but here instead of usual t(0.975, df) quantile, you > should use the moderated t quantile ie t(0.975, df.residual + df.prior) > > So the 95% CI for logFC will be > > logFC -+ t(0.975, fit3$df.residual + fit3$df.prior) * fit3$stdev.unscaled * > sqrt(fit3$s2.post) > > > Please correct me if I am wrong. > > > Thanks, > S. > Hi Sunny: sorry for the very late reply. Is fit3 the return value from eBayes()? Timothy [[alternative HTML version deleted]]